The Reaper War
by RetroRebel85
Summary: When Earth falls, the job of uniting the galaxy falls into Commander Shepard's hands. A complete retelling of Mass Effect 3 with most cut content returned to it's full glory, and including Leviathan, Omega and Citadel. Major spoilers ahead. Rating may change.
1. The Fate of the Galaxy

**The Reaper War**

**Prologue: The Fate of the Galaxy**

_**Location: Sol System, Earth. Vancouver, Canada. **_

The sunlight cast through the windows of the interrogation room, a steel box surrounded by a mass effect field to prevent anyone leaving. In its centre sat a table, several datapads and a cup of cold, foul-tasting coffee placed upon it. On one side was a man in handcuffs, a shaved head and heavily scarred face looking down at the faces in front of him on the datapad's digital display, and on the other sat an interrogator. The interrogator, an immaculately dressed Alliance officer, stared down his nose and over his glasses at the handcuffed man in front of him. "John Shepard."

Commander Shepard looked up from his intense study of the information, nodded silently and concentrated on the officer, who spoke again in a nasal and somewhat arrogant tone. "Former Captain of the SSV Normandy, the "First Human SPECTRE", officially announced dead in early 2184, arrested for charges of treason, destruction of Alliance property, destruction of a mass relay and the subsequent deaths of every living being in the Aratoht system. How do you plead?" he asked, giving the Commander an inquisitive look, putting a line on his already wrinkled face. Shepard looked ahead, showing no emotion other than regret for the Alpha Relay incident. He began to speak, but then stopped. "Actually, let's begin from the start. Your service record says earthborn date of birth 11th April 2154, no record of any family members. Why enlist?"

"It was either enlist or live in the dirt and die that way." The officer seemed content with the answer. "You served on Elysium as part of your N7 training. What happened there?"

"You know the answer, Colonel. Batarians. Me. Saviour of a colony. Singlehandedly protected everyone." Shepard replied. He'd already told the story to three reporters, Admirals Hackett and Anderson, Miranda Lawson and Liara T'Soni.

"Yes, I do, but the real point of this exercise is finding out what do you remember? From what I recall, you were effectively re-created from very little. We have to ensure that you are the real Shepard, and it's just a precaution."

For another hour, the two men discussed the true story of Commander Shepard up until the Battle of Virmire. "You were forced to leave Lieutenant Kaidan Alenko behind. Why?" Shepard remembered the look on Ashley's face, standing on the balcony beside him and Garrus Vakarian when they had to retreat. "I left a friend to die that day and I didn't do it casually, but I had to save as many people as I could. Kaidan gave his life for the rest of the team. Without him, I couldn't have stopped Saren. He died a hero." A wave of déjà-vu washed over him, the memory of his mental test after waking up in the Cerberus facility. His thoughts drifted briefly to Miranda and Jacob, who became the next topic of conversation.

"For the last three months you were working with Cerberus, volunta-" he began, but was quickly interrupted by Shepard. "It was really more a case of common interest. If you read those files, you can see I forwarded as much information as possible to the Alliance and the Council. My crew and Normandy left Cerberus when I did." Said John. "The crew that survived?" asked the officer. John looked down at his hands.

"Yeah… we lost three good people, and some of our squad didn't get a chance to do what they really needed to."

"What could they need to do?"

"Just things they wanted to settle before they went on the mission."

"I see… who did you lose?"

"Jacob Taylor, Zaeed Massani, Kasumi Goto." Shepard named them quickly, having thought about his team a lot over the last six months.

"A terrorist, a mercenary and a thief. Hardly what I'd call 'good people'."

John looked up, the implants given to him by Cerberus starting to throb and glow faintly under his skin. He scowled, remembering what remained of Jacob's body, Zaeed's dying words and how Kasumi never even got to say goodbye before she was vaporized. "They died helping me save people like you, so unless you're ready to argue with me, you should watch your Goddamn mouth. If you've got any more idiotic questions, hurry up and ask me them. Otherwise, I'm done talking."

The officer adjusted his crescent-shaped glasses. Shepard rattled his cuffs and within a few minutes the Commander was led back to his cell. Shepard sat down on the hard bed; staring out the window and watching the fighters fly back and forth through Earth's atmosphere. He looked ahead, wondering where Normandy was being re-integrated into Alliance systems. He cursed himself for allowing the outburst of rage earlier, yet felt a slight sense of pride; he'd contained his biotics at least.

**Location: Widow System, SSV Gettysburg. **

Admiral Steven Hackett removed his cap and ran a hand through his white hair. It had been two weeks since Commander Shepard's questioning, and the recent disappearance of two deep space outposts, in light of the description of the Collector Base, was disconcerting. As Hackett looked up in the Conference Room, Admiral David Anderson appeared on his desk. "Anderson." Hackett greeted him, the blue outline of the small, toy-like figure of the Admiral saluting in turn.

"Hackett. How bad is it?"

It was almost as if Anderson could read his mind.

"Bad. We just-" he began, but David interrupted.

"I know, Udina told me. Is this what Shepard warned us about? The Reapers?"

As soon as the name was mentioned, a shiver ran down Steven's spine.

"I don't know, Dave, but there's something massive on the long range scanners."

In the main body of the ship behind him, officers and crewmen hurried about the deck, attending to terminals and interfaces. There was a long, uncomfortable silence in the Conference Room. Anderson broke the quietness: "How long do we have?" he asked.

"Not long. I've sent word, and the fleets are mobilising." Hackett replied.

He looked to his left, out of the window as the viewpoint changed from a vista over the Citadel to Earth, surrounded by satellites and Alliance warships.

"God help us all…" Anderson breathed, and ended transmission abruptly.

**In 2157, humanity discovered it was not alone in the universe. **

**Thirty years later, they found a peaceful place among dozens of galactic species. But this idyllic future is overshadowed by a dark past; the Reapers, a sentient race of machines responsible for cleansing the galaxy of all organic life ever 50,000 years are about to return. The leaders of the galaxy are paralyzed by indecision, unable to accept the legend of the Reapers as fact. But one soldier has seen the legend come to life. And now, the fate of the galaxy depends on him.**


	2. The Assembly

**Chapter One – The Assembly**

**Location: Sol System, Earth. Vancouver, Canada.**

A young boy, aged around 7 or 8 was playing with a toy Alliance fighter in a rooftop garden several miles below the Vancouver skyline, which had grown considerably since humanity discovered the first mass relay. As a UT-47 Kodiak Shuttle flew past the window, Shepard smiled at the sight, but then became deeply concerned. None of the people in this city, let alone the world, were aware that any day now, the Reapers would arrive and begin their harvest. He frowned, lifting a datapad off the shelf in the room. He began to study the contents, the same information Joker had forwarded to him six months ago after the Suicide Mission. The datapad contained extensive information on Harbinger, the other Reapers, how they moved and the true fate of the Protheans. He sat down, rubbing the patch of stubble on his chin. Looking up from the device, the door shifted open. In its place stood a hulking, built Latino man, scarred but well wearing an Alliance Special Forces shirt.

"Commander." The marine saluted, his dog tags dangling from his neck over his shirt, and Shepard half-smiled and saluted back.

"You're not supposed to call me that anymore, James." He said.

"Yeah, not supposed to salute you either… we gotta go. Defence committee's waiting for you." Replied James.

"Sounds important." Said Shepard.

James walked out of the room hastily, so quickly that Shepard had to jog lightly to catch up. The two soldiers walked through the halls of the Alliance base, dodging officers running around and reporters in the building.

"What's going on?" asked Shepard, trying to start a conversation longer than ten seconds.

"You tell me, hell if I know. All they told me was that you were needed, pronto."

As they reached the end of Detention Center Block B, Shepard stopped in his tracks. Coming up the stairs was a familiar face, a sight John grinned at.

"Shepard!" Admiral Anderson greeted him. Shepard put his hand to his forehead respectfully and James also saluted, but Anderson didn't seem to notice. His hair had greyed and the stress was evident on his dark-skinned face from the wrinkles cast over his forehead and cheekbones.

"You look good, Shepard. Maybe a little soft around the edges." He joked, patting the Commander's stomach. Subconsciously, John put his hand to his belly; he hadn't exercised in the way he did aboard Normandy for six months. "How're you holding up with being relieved of duty?"

Shepard laughed. "Well, once you get used to the hot food and soft beds, it really isn't that bad."

"Don't worry; we'll get that sorted out."

"What's going on?" asked John.

David turned to look at him properly, a darker expression on his face than the smile he had worn earlier.

"Admiral Hackett's mobilising the fleets. I'm guessing word's made it to Command… something big is headed our way."

Shepard looked at him, and without saying a word Anderson knew exactly what was going through his head.

"We think… we think it's the Reapers. But we don't know for certain, right?" he said.

"Oh come on, what else could it be?"

"If only we knew."

"Anderson, if it really is them… we aren't ready. We aren't ready at all."

Shepard grimaced at the fact. The Alliance had already delayed a Reaper invasion at the cost of a massive amount of several Alliance fleets, and then Shepard and the crew of the second Normandy had stopped another invasion by about six months, but in the process had destroyed an entire system of batarian inhabitants.

"Tell that to the defence committee." Anderson rolled his eyes at the thought, both of them and James, who had remained silent, walking up a flight of stairs.

"Unless we're planning to talk the Reapers to death, having an assembly is a waste of time!"

"They're just scared. None of them have seen what you've seen. You faced down a Reaper… hell, you spoke to one and then you blew the damned thing up!" said Anderson, a tone of awe in his voice as he spoke. "You and your team know more about this enemy than anyone in the galaxy."

Shepard stood in his way, visibly annoyed. "Is that why they arrested me? Took away my ship?"

Anderson's face became like that of an angry parent reprimanding a child for arrogance.

"You know that's not true. The shit you've done? Like blowing up the Alpha relay, killing hundreds of thousands of batarians in the process?"

"It was that or let the Reapers walk in through our back door!" Shepard argued.

"I know that, John, and so does the committee. If it wasn't for that, you'd have been court-martialled and left to rot in the brig."

"Yeah, that and your good word?" asked Shepard, sarcastically.

"I trust you Shepard, and so does the Alliance."

"Anderson, I'm a soldier. Not a politician."

"Frankly, son, I don't need you to be either. I just need you to do whatever the hell it takes to stop the Reapers." Anderson said, walking the Commander towards a scanner as James took a seat outside.

When they approached the desk, a woman turned around. She had reddish-brown hair and a pale complexion. "They're expecting you two, Admiral." She said, leading them into the main room. At the far end, a woman with long, dark hair and a blue suit walked towards them. "Anderson." She greeted the Admiral, but Shepard had his back turned.

"John!" she smiled, regaining her composure afterwards. Shepard turned to her, in disbelief at the transformation she had undergone in six months. Ashley Williams was originally much more tomboyish in looks, her hair done into a bun to prevent it interfering with her aim. She seemed to had lost the Phoenix armour, a pink and white colour scheme that Urdnot Wrex had shown particular distaste for.

"Ashley. Long time no see, eh?" He said, remembering their bitter reunion on Horizon during his time with Cerberus.

"How'd it go?" Anderson asked her.

"It's High Command, boss, you can never tell with them. I'm basically just waiting for orders now."

"You'll be fine, Lieutenant-Commander."

Shepard raised an eyebrow. "LC?"

"You hadn't heard?" Anderson said, surprised.

Shepard looked at him incredulously, and said, "No, I'm a bit out of the loop these days."

Ashley appeared almost upset.

"Sorry, sir. I didn't mean to keep you out of it."

John looked to her now, his eyes scanning her face.

"It's okay. You probably had your reasons."

She nodded, and held out her hand. "Yeah, I guess I did. Still, it's good to see you again."

Shepard took her gloved hand and shook it gently, smiling at her. As the red-haired woman beckoned them over, Shepard excused himself and Anderson and they walked past Ashley and into the room. James, who had been watching the meeting, spoke to her.

"So… you knew the Commander?"

"Used to. Were you assigned to Normandy?" she asked him, and with the affirming nod he gave her, they made their way to the ship.

Inside the Alliance Council Room, a massive window overlooked the docks of Vancouver, and Shepard could just barely see Normandy's tail behind it. It towered over them, and Shepard recalled how the Citadel Council Chambers had a room just like this. He could also see the officer who had interrogated him, alongside several other high ranking officials. Admiral Hackett, he noticed, was not present.

"Where the hell is Admiral Hackett?" Anderson half-whispered to himself, just loud enough to catch John's attention. Each of the councillors stood to attention as they became aware of Shepard and Anderson's presence.

"Admiral Anderson, Shepard." The head of the committee greeted them. Shepard spoke first.

"What's the situation?" he asked

"We… were hoping you could tell us." The chancellor said.

Another councillor, an elderly woman with white hair, spoke up. "The reports coming in are unlike anything we've ever seen. We've lost contact with everything beyond the Sol relay."

"Whatever this is, it's incomprehensibly powerful." The chancellor said.

"You summoned me to confirm what you already know," said Shepard, looking at them and then to the datapad in his hands, "The Reapers are here."

The committee, at the very mention of the word, were in uproar. Anderson shook his head in disappointment, but Shepard noticed that it wasn't the same kind of arrogant disbelief the Citadel Council had shown him. This was panic; the Alliance knew too well, as did Shepard, that they weren't ready. As the talk died down, the councilwoman began speaking again.

"Then how do we stop them?"

Shepard and Anderson looked at each other briefly, then turned back to face the committee.

"Stop them?" Shepard said, coldly. "This isn't about strategy or tactics! This is about survival!" John began walking towards their long, rounded table. "The Reapers are more advanced, intelligent, and powerful than we are. They don't feel fear, and they will _not_ pity us."

"But there must be some way!" the female councillor said again, fear evident in her voice.

"For any chance at defeating them, we have to stand together."

The chancellor looked at him bemusedly and began shouting.

"That's it? That's your grand plan?!"

The red-haired woman that had led them in interrupted the brief, one-sided argument.

"Admiral, we've just lost contact with Luna base!"

"The moon… they couldn't be that damn close already…" Anderson looked to the skies behind the council, in total disbelief.

"Sir, UK Headquarters has a visual." The woman called across the room.

A large screen descended from the roof, a display on both sides. She typed a command into her omni-tool and a static mess appeared onscreen. A man, set against the backdrop of Westminster Tower in Alliance uniform, was shouting an unintelligible string of words at the camera. The expression on his face was that of pure terror, his voice growing increasingly louder and more desperate. The entire room was deathly silent, as the chaos on the display met their eyes. Suddenly, a mechanical whirr began to sound through the speakers, and the video was engulfed in flames and smoke. As the camera toppled over, the source of the noise was confirmed; amongst ruins and burning buildings, a Reaper was stomping through Westminster, the red beam emitting from its cannon decimating any resistance.

The feed cut out entirely, and the signal was lost, but almost instantly replaced by hundreds of Alliance News Network videos. Shepard scanned over all of them, scenes of devastation all over Earth. Paris, Berlin, Rome, London, Washington, Madrid, Tokyo… every single one of Earth's cities being systematically overrun.

Anderson turned to Shepard, asking "Why haven't we heard from Admrial Hackett?"

Shepard looked concerned, which turned to anger.

"What do we do?" asked the chancellor, his face pale.

"We fight or we die; those are the options!" John shouted. Anderson pulled up his omni-tool and spoke to it.

"Moreau, get Normandy to our position ASAP."

"Aye aye, Admiral." Came the voice on the other end.

Everything stopped. The ground beneath them began to shake, and they became painfully aware of the deep, unsettlingly loud rumbling coming from the skies. The committee members rose from their seats and stood by the window, and it was at that moment that Shepard realised exactly why windows were a structural weakness. The skies began to flash with what seemed like scarlet coloured lightning.

Down from the clouds descended a machine so massive it appeared to block out the sun itself. Each of its components clicked and whirred in tandem as its firing chamber slid back, and revealed a giant metallic cannon. John and David both began shouting at the same time to run, but it was too late. Within milliseconds the Reaper opened fire on the building, and chaos erupted, a crimson ray of death slicing the chamber neatly in half. The sheer force of the shattering window sent the members of the committee flying backwards, the chancellor dying instantaneously as he was burnt alive by the beam.

Shepard turned, grabbing Anderson and running for the door, realising there was no hope to save the rest of the committee when their grand table flew into the air, ungracefully, and came down again. As it rolled furiously down the room, Shepard and Anderson both found themselves on the floor, John covered by the body of the red-haired woman. The Reaper seemed pleased with the attack, and left the rest of the work to the smaller fighters that had landed, whom were already tearing apart what they could find. The room exploded again, lifting Shepard off his feet and into the wall behind them. He lay there in a state of shellshock, listening to the screaming and the sound of the Reaper's cannon firing repeatedly at other buildings. His vision began to fade and his eyes closed slowly, but the sharp kick Anderson delivered to his side woke him up.

"Take this," he said, handing him an M-3 Predator pistol he'd scavenged off a guard nearby. "We've got to get moving."

They stood at the edge of the hole formed by the blast, looking over the docks. Despite the scene previously, Shepard finally realised the reality of the situation.

The Reapers were on Earth.


	3. The Invasion

**Chapter Two: The Invasion**

**Location: Sol System, Earth. Vancouver, Canada.**

"They're massive!" Anderson gasped, as the two men watched the Reaper that had recently tried to kill them in the distance. The Admiral signalled for Shepard to follow him, as they ran carefully along the edge of the ruined Alliance Canadian Headquarters, small fragments of metal sticking out like nails in a plank of wood. "Come on, Normandy's on her way to the spaceport."

A Reaper Destroyer overhead opened fire on another target, the beam momentarily blinding Shepard as it caused an explosion below. They curved around the building's roof, leaping over an exposed section.

Anderson's stamina and speed surprised Shepard, who could just about keep up with him. They reached a ladder, letting David take point. Both men were quiet, panting as they climbed and then immediately took off sprinting again. Shepard looked off in the distance, catching a glimpse of the other Reapers in the city. A sudden crackle alerted Shepard to his omni-tool, and from it came Ashley's voice.

"Shepard, Anderson? We're almost to the Normandy. I brought Vega with me but we're under some heavy fire!" she said, keeping her cool despite the circumstances. The audio ceased, and on the building ahead Shepard saw what looked like people crawling up the walls. On the balcony below them, the same boy Shepard saw playing earlier on ran for his life into the apartment. John hoped he would be safe in there.

"Husks!" Anderson called, firing a few shots at them. Shepard followed the example, standing still and aiming for the head. Anderson dropped down another ladder, and charged at one of the husks, caving its head in with the butt of his pistol.

"I'm out, any spare clips?" he asked Shepard, who responded by dropping the empty clip out of his own pistol and loading one bullet into the chamber. Another wave of husks appeared at the balcony's railing, and Anderson rushed one of them again, beating it with his gun. Shepard pulled his arm back and unleashed a biotic throw, one husk colliding with another and sending them both flying down into the streets below. The Reaper that had been terrorising the Alliance District turned, as if it was aware of the dead husks. It opened its firing chamber with a roar and blasted the apartment beside them, showering the men with glass and mortar. Rising to their feet, Anderson checked Shepard for major injuries and moved inside the building.

"We gotta find a way out of here…" said David, moving towards the door in the far corner of the room. It opened, and Anderson jumped back just in time to avoid being clawed by the enemy in the doorway. It was trapped between the doors, desperately scratching at the air. Shepard fired his last round at the husk, and it dropped dead onto the ground. Anderson pulled at one side of the door, letting Shepard take the other.

A movement alerted John to the vent in the back of the room. He aimed his gun at it, moving slowly to the opening. Crouching down, he noticed the boy from earlier crawling backwards inside the vent, and he dropped the gun to the floor to avoid frightening him.

"Hey, are you okay?" John said, trying to smile. The boy had clearly been crying, his eyes puffy and red.

"Everyone's dying..." he sniffed, wiping the tears from his eyes with his jacket sleeve. The child gasped, and Shepard turned to see the Reaper's leg disappear from view.

"I can get you somewhere safe, I promise. Take my hand." Shepard held out his hand to the boy, but he backed away.

"You can't help me." He said. Shepard was taken aback by the sentence.

"What?" he began to ask, but then Anderson returned.

"Shepard! In here." David beckoned him into the other room, having found a safe exit. John turned to the boy, but he had vanished without a sound. His last few words puzzled him, but Shepard had little time to ponder everything.

Anderson navigated along the precarious ledge he had cleared, ranting angrily. "Every minute these machines are here, thousands of innocent people die, and I won't be responsible for it."

Shepard sympathised.

"It's hard enough fighting a war, but it's worse knowing that it doesn't matter how hard you try; you just can't save everyone."

"Exactly…" Anderson murmured, crawling out into the sunlight again.

"They came so fast!" he growled, lifting a thermal clip off the ground. In the light, blood shone on his dress blues, and Shepard's clothing while he was incarcerated was dirty and torn from the explosion.

"We knew they were coming."

"Yeah, and they still cut through our damn defences! We need to talk to the Council." Said Anderson.

"The Citadel? Anderson, the fight's here."

"You said it yourself; the Reapers will destroy everything if we don't stop them."

Shepard also reached for a thermal clip, loading it into the Predator.

"You're still a Council Spectre, that's gotta count for something at least."

"Thanks, Anderson. I owe you one."

"You owe me more than one, son." David replied.

They ran through a small garden and charged down the side of the apartments, a transmission from Ashley coming in.

"Admiral, we've made it to Normandy, still taking some- Oh, God! They're gonna take down that dreadnought! Joker, evasive manoeuvres!" she shouted, as Shepard and Anderson both stopped to observe the SSV Kilimanjaro exchanging fire with the Reaper that had dogged them previously. As the Reaper fired its beam, the back of the dreadnought lit up with a dazzling blue light. Shepard braced himself; the mass effect core then promptly exploded, destroying the ship entirely. The force of the destruction rocked the platform Anderson and Shepard were on, sending them both tumbling painfully down to the ruins below. Shepard heard his name being called again, as he and Shepard both crawled out from under yet more wreckage. The war hadn't even fully began and already John was sick of it, moving to cover as they noticed four red enemies on the other side of the bridge they were at. To their right lay a seriously wounded marine, being tended to by a medical crew who were exchanging shots with the creatures.

"What the hell are these things?" asked one medic, the marine groaning in pain beside him.

Shepard peeked over cover at the enemies, grotesque mutations of what looked like batarians, owing to their four eyes. Their faces seemed permanently fixed in a scream, and their bodies were covered in the same Reaper machinery as the husks. Anderson and one of the medics began pulling the marine from the wreckage as Shepard and the other soldier exchanged fire with the batarians. As the last one fell, the marine was dragged free and the bridge lowered.

"Come on, I'll tell Normandy we've rerouted!" said Anderson, signalling the ship and leading the way across the bridge. After a brief period of running, they took cover at another wall and observed the batarian husks, spotting a radio and an Avenger rifle on the other side of a piece of the dreadnought that had just been downed.

"They're… eating?" Shepard said, watching them devour a fallen ally, and as they did they took parts from the corpse and attached it to themselves. Anderson fired, but the bullet bounced off their organic armour. Alerting their attention, David gave covering fire as Shepard climbed onto the right wing of the SSV Kilimanjaro nearby; quietly running to the rifle and radio.

Anderson's thermal clip jammed, and the fire continued from the batarians. He heard a whistle, and looked up to see gunfire spray towards them as their attention turned to Shepard on the other side of the wall. This gave him the perfect time to reload and fire again, but then they were swatted away by a biotic shockwave. Shepard returned to Anderson, and began firing on the remaining batarians as David called Normandy for evac. A sudden silence startled them both. They reloaded and checked their thermal clips during the pause, as Shepard rubbed his right temple.

"That can't be good." Anderson muttered. The air was calm, and the Reaper was off in the distance. The sky began to crackle red again, and a ball of fire exploded onto the ground in front of them.

"Run!" Shepard shouted, diving into a covered position and blind-firing the Avenger over the wall. Anderson loaded a Concussive Shot onto his pistol, firing towards the batarians and scattering them, but when they fell they were replaced by more. Shepard was slowly becoming more exhausted as his biotics began to wear thin; he wasn't a natural biotic, wasn't trained at BAAT like Kaidan. His implants were done during the Lazarus Project, and hadn't been fully introduced to his nervous system yet. As he pushed the final amount of energy outwards, the troops flew violently backwards. He pressed himself against the cover, and the batarians seemed to spawn endlessly. Anderson threw his gun away, drained of ammunition. A familiar droning came from the skies, and a bright flash of orange light lit up the clouds.

"Cavalry has arrived, gentlemen!" cheered Normandy's pilot, Jeff 'Joker' Moreau. A salvo of missiles decimated the reaper forces, and Normandy came into view, her majesty and grace still present; but her orange, black and white colour scheme supplied by Cerberus had gone, replaced by the Alliance white and blue. Shepard grinned, proud to be back with his ship, as he took off with Anderson towards the cargo bay's opened ramp. When he neared it, there stood Ashley and James, firing shots at whatever husks had survived Joker's attack. Shepard leaped aboard, looking to Ashley.

"Welcome back, sir." She smiled at him, and Shepard nodded in response.

"Thanks."

Anderson caught up to him, standing on the edge between Normandy and the ground. The waves below them roared due to the ship's forces, splashing David.

"What are you waiting for?" Shepard asked him.

Anderson looked around at the ruins behind him. A Kodiak shuttle flew past, landing where they had made their stand.

"I'm not going. You saw those men back there, and there's a million more like them. They need a leader!"

"We're in this fight together, Anderson!" Shepard shouted.

"You're smart enough to understand this, John. Go to the Council and get help for Earth, and that's an order!" he yelled back.

"I don't take orders from you now, remember?"

Anderson reached into his inside pocket and pulled out a pair of dog tags. They had the N7 emblem engraved onto one side, and Shepard's information on the other. Anderson looked at them one last time, throwing them to Shepard.

"Consider yourself reinstated; Commander!"

Shepard clutched them, putting them around his neck afterwards.

"I'll come back, and I'll bring every fleet I can!" Shepard called to him.

"Good luck, John." Anderson saluted.

Shepard returned the favour, saluting him. "Likewise, Anderson."

Admiral Anderson turned and ran back down the ledge towards the Kodiak, taking off with them. On the ground, Shepard saw the survivors from the apartment block running for the shuttles.

"No…" he whispered, seeing the boy from earlier try to keep up with the others. Ashley turned to him, trying to look in the same direction as the Commander.

"Help him!" Shepard shouted, but he couldn't be heard from that far away. The Alliance soldiers protecting the shuttles saw the child, lifting him onboard and shutting the doors. Shepard breathed a sigh of relief… but then he saw the Reaper re-emerge from behind the apartment buildings. The shuttles took off, and the same beam that had tried to kill him fired one final time, hitting both of them in rapid succession. Shepard looked away as they exploded, pale faced. He looked back, his anger towards the Reapers finding a new high. For three years, he had tried to warn the galaxy about their threat, and now they were here in full force. Ashley moved towards him, James still watching the chaos in Vancouver with horror on his face. Shepard turned, and walked to the armour locker to retrieve his N7 armour. Vengeance for Earth would have to wait.

For now. Normandy flew upwards and onwards, exiting Earth's atmosphere as more Reapers made their way towards the planet. Her stealth systems engaged and the Reaper IFF activated, Normandy was but a speck of dust on the solar winds to the ancient, eldritch enemy.


	4. Mars

**Chapter Three: Mars**

**Location: Sol System, Luna**

Normandy's cargo bay hummed with the noise of her engines running. The peace and quiet was calming for Ashley, especially after what had just happened on Earth. She mused over her promotion, Shepard's disappearance, his arrest, Horizon, everything. Cleaning the barrel of the Avenger rifle she was given as standard, she watched as Shepard sat on the floor of Normandy's Kodiak shuttle doing the same.

"Are you okay?" she called to him. He looked up, nodded, and continued fiddling with the gun. She sighed outwardly, and behind her in the elevator shaft appeared James, who stormed out towards the Commander. With the passion she would expect from a Latino soldier, he began to speak.

"What the hell's going on? Where's Anderson?" he asked, stopping in front of the shuttle. John looked up again, setting his rifle by his side, and stood before James. They were about the same height, he noticed. Shepard said nothing, walking to where his armour lay.

"Hey!" shouted the marine.

"We're leaving."

"Leaving?!" James parroted Shepard's words, his voice cracking. Ashley turned around from her position at the gun bench.

"What's going on?" she asked.

"Anderson wants us to go to the Citadel, and get help for the fight."

"He wouldn't just order us to leave…" said James.

"Without help, we've already lost." Said Ashley. John stood his ground, as James began to shout. "Fine, drop me off some place, because I'm not leaving!"

Shepard pointed his finger at him, matching his volume.

"Stow it, Lieutenant! Don't you think I'd rather stay and fight too?"

James said nothing. "We're going to the Citadel; you want off, you can catch a ride there."

James muttered curses under his breath in Spanish, walking away to the other end of the cargo bay. John shook his head, irritated, yet fully understanding his anger. He himself didn't like this idea. The intercom buzzed, and out came Joker's voice.

"Message from Alliance Command, patching it through."

The terminal near the elevator lit up, displaying Steven Hackett's grizzled face.

"Admiral?" Shepard said, trying to clear up the poor quality audio.

"Shepard, divert from the Citadel! Head to…Mars… Dr T'Soni… Cerberus interests…" was all John managed to get out of the transmission, losing signal entirely. The Reapers must have been jamming their communications.

"I've set a course, boss." Said Joker, flying the ship to the Prothean archives on Mars.

"Why Mars? What does he think we'll find there?" Ashley said to no-one in particular.

"I don't know, but if it helps us win this war…"

**Location: Sol System, Mars. Prothean Research Outpost.**

"_Hey, I've been trying to reach Mars on secure channels but there isn't an answer, Commander." _Joker's face appeared on the dashboard of the shuttle, speaking to Shepard. James sat in the pilot's seat; their shuttle pilot wasn't onboard Normandy when they were leaving Earth.

"Any sign of Reaper activity?" asked Shepard.

"… _negative, boss." _Came the reply. Remembering Normandy's Artificial Intelligence, Shepard spoke again, to a different subject.

"EDI?"

"_The base appears to be online. It is possible the inhabitants were evacuated." _Said the AI. After an attack on the Normandy SR-2 by Collector forces, Joker was forced to unshackle EDI to save the ship. After proving EDI was not hostile in any way to the crew, they eventually warmed up to it. Professor Mordin Solus was particularly impressed with it.

The Kodiak glided peacefully to the dusty surface of the 'red planet', settling in an open space of land near some solar panels.

"So let me get this straight; Anderson wants us to go get help, but Hackett wants us to go to Mars and can't explain why?" asked James to the group, consisting of him, Shepard and Ashley. The three exited the shuttle, fixing their oxygen supplies and taking note of the massive wall of dust in the distance.

"It's not that he couldn't, Lieutenant, the communication was interrupted," answered Ashley, attaching a scope to her Argus assault rifle, "By the way, Commander, we should hurry up; we've got at least half an hour before that storm starts interrupting comms."

Shepard took point, reaching a small cliff and lowering himself down to the ground from it. To his right lay a dead marine, a Mantis sniper rifle beside him. Ashley, upon hitting the ground, began to scan his records with her omni-tool.

"Alliance, Sergeant Reeves. Doesn't look like he put up a fight…" she mused, taking the rifle and modifying the identification tag on it so she could use it. Moving ahead, Shepard walked into the open, looked to his left and darted back into cover. Towards the base entrance, four scientists were on their knees with their hands behind their heads. Shepard couldn't hear what the soldier behind them was saying, but the white, black and orange colours were instantly recognizable.

Cerberus.

His former employers probably wouldn't take kindly to him stealing their ship, their AI and some of their best staff.

"Ash, mark the-" he began, being interrupted by the sudden BANG of a Carnifex being unloaded into a human skull. Shepard peeked out, the three remaining scientists being executed in the blink of an eye. Ashley loaded the Viper, James readied a Carnage round into his Mattock and Shepard was ready with an Avenger. As the executioner turned his back, his men stood to attention and were promptly sprayed with his grey matter, as the Viper pierced his helmet on both sides and destroyed his head. James fired his Carnage, triggering an explosive round upon impact and then following the distraction with sustained fire, letting Shepard flank with the Avenger and eliminate any remaining foes. Once all was done and the gunfire had settled, Ashley spoke up.

"Was that Cerberus?"

"Yeah."

"What were they doing here?"

"You say that like I should know."

"And you don't?"

"I don't work for them anymore Ash, if that's what you're thinking." Shepard said, annoyed at her lack of trust.

They moved forward and took cover at two Cerberus APCs, listening to the troopers behind them speaking.

"Did you see that?" one said, sounding panicked. The sound of an M5 Phalanx being loaded came from the same source as the voice.

"James, door." Shepard commanded the marine to move closer to the facility's entrance. He stumbled on a loose rock, alerting the Cerberus soldiers to his presence.

"Freeze!" they shouted in unison, their vocal filters making them sound deeper and more aggressive. James slowly dropped his rifle, raising his hands above his head. Ash went to move up, but Shepard froze, noticing a glint of glowing azure underneath the facility's sliding door.

"Alright, here I am, just me!" James shouted, sounding more mildly irritated than fearful.

"It's not just you, where is she?"

Ashley moved to a better position, letting Shepard take the right flank.

"Where's who, _pendejo?_" the Lieutenant snarled through his mask.

"The asari!"

Shepard looked over to Ashley, who was equally as confused.

"Maybe you can come over here, _cabrón,_ and tell me all about her." James said, sounding genuinely friendly.

"What the hell is he doing?"

They had no time to act, as when they looked back, both men were levitating in the air.

"Holy shit, a biotic?!" the two troopers yelped in fear, as the singularity field keeping them off the ground expanded and threw them to the floor. In one swift and sleek movement, an asari in a lab coat moved forward and executed both of them.

James picked up his gun, pointing it at her, as did Ashley. Shepard stood up and walked into the open.

"I was wondering when you would get here, Commander." She smiled, holstering her pistol.

"Sorry I kept you waiting, Liara." Shepard returned the smile, shaking hands with his old friend.


End file.
